BioC 3.2: CHECK report for INSPEcT on perceval

Package: INSPEcT

Version: 0.99.8

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings INSPEcT_0.99.8.tar.gz

StartedAt: 2015-08-24 01:54:41 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 02:02:51 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 489.8 seconds

RetCode: 0

Status:  OK

CheckDir: INSPEcT.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings INSPEcT_0.99.8.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/INSPEcT.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘INSPEcT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘INSPEcT’ version ‘0.99.8’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘INSPEcT’ can be installed ... [22s/22s] OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [521s/232s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
modelRates         65.747 26.542  54.288
makeSimModel       39.089 36.082  29.542
makeSimDataset     36.968 34.584  26.183
newINSPEcT         28.616 32.864  15.938
ratesFirstGuess    26.386 30.799  17.800
sfPlot             25.300 27.558  13.431
ratesFirstGuessVar 25.582 26.822  14.876
rocThresholds      35.052  0.141  35.369
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/INSPEcT.Rcheck/00check.log’
for details.

* installing *source* package ‘INSPEcT’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (INSPEcT)

name	user	system	elapsed
AIC-INSPEcT-method	0.014	0.007	0.020
Extract	0.125	0.007	0.131
chisqmodel	0.044	0.006	0.058
chisqtest	0.011	0.007	0.018
combine	0.183	0.007	0.191
geneClass	0.060	0.005	0.065
getModel	0.010	0.005	0.015
inHeatmap	0.047	0.006	0.053
labeledSF	0.010	0.006	0.016
logLik	0.012	0.006	0.018
makeGtfFromDb	2.038	0.450	4.598
makeModelRates	0.863	0.060	0.928
makeRPKMs	0.003	0.000	0.004
makeSimDataset	36.968	34.584	26.183
makeSimModel	39.089	36.082	29.542
modelRates	65.747	26.542	54.288
modelingParams	0.020	0.051	0.071
nCores	0.025	0.052	0.078
nGenes	0.01	0.02	0.03
nTpts	0.009	0.021	0.031
newINSPEcT	28.616	32.864	15.938
plotGene	0.049	0.038	0.087
ratePvals	0.100	0.104	0.205
ratesFirstGuess	26.386	30.799	17.800
ratesFirstGuessVar	25.582	26.822	14.876
removeModel	0.082	0.034	0.115
rocCurve	3.575	0.335	3.923
rocThresholds	35.052	0.141	35.369
sfPlot	25.300	27.558	13.431
split	0.122	0.093	0.215
testingParams	1.661	0.348	2.011
totalSF	0.009	0.016	0.025
tpts	0.009	0.015	0.023
viewModelRates	0.011	0.017	0.028